ENST00000433230.1:n.136+167G>C

Variant names:

• chr22-38424590-G-C
• rs5757091
• ENST00000433230.1:n.136+167G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000433230.1(ENSG00000228620):​n.136+167G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0463 in 152,220 control chromosomes in the GnomAD database, including 392 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.046 (392 hom., cov: 32)
• Consequence: ENSG00000228620 ENST00000433230.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570
• Publications: 2 publications found

Genes affected

ENSG00000228620 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927183	XR_938252.3	n.146+167G>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228620	ENST00000433230.1	n.136+167G>C		intron_variant	Intron 1 of 2	2
ENSG00000228620	ENST00000776849.1	n.93+167G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0463 AC: 7038 AN: 152102 Hom.: 387 Cov.: 32

Gnomad AFR AF: 0.0704

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.00576

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.0240

Gnomad FIN AF: 0.0238

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00885

Gnomad OTH AF: 0.0568

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0463 AC: 7055 AN: 152220 Hom.: 392 Cov.: 32 AF XY: 0.0485 AC XY: 3609 AN XY: 74420

African (AFR) AF: 0.0705 AC: 2926 AN: 41528

American (AMR) AF: 0.130 AC: 1981 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.00576 AC: 20 AN: 3470

East Asian (EAS) AF: 0.197 AC: 1020 AN: 5166

South Asian (SAS) AF: 0.0240 AC: 116 AN: 4826

European-Finnish (FIN) AF: 0.0238 AC: 253 AN: 10620

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00887 AC: 603 AN: 68006

Other (OTH) AF: 0.0624 AC: 132 AN: 2116

Alfa AF: 0.0283 Hom.: 20

Bravo AF: 0.0559

Asia WGS AF: 0.107 AC: 375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.70
DANN	Benign	0.53
PhyloP100		-0.057
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs5757091; hg19: chr22-38820595;